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   <div id="projectname">IEEE-Std-1906
   &#160;<span id="projectnumber">0.0</span>
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   <div id="projectbrief">Implementation of simple microtubule structure</div>
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<div class="title">Todo List </div>  </div>
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<div class="textblock"><dl class="reflist">
<dt><a class="anchor" id="_todo000011"></a>Namespace <a class="el" href="namespacens3.html">ns3</a>  </dt>
<dd>remove before submitting  </dd>
<dt><a class="anchor" id="_todo000002"></a>Member <a class="el" href="classns3_1_1_p1906___metrics.html#a572720a0a00101084f8805e578181d75">ns3::P1906_Metrics::Active_Network_Programmability</a>  (gsl_matrix *vf, gsl_vector *pt)</dt>
<dd><p class="startdd">consider using vector field and divergence to compute this value </p>
<p class="enddd">see double <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___vol_surface.html#ab9de294ac38ab43f4ea3a19d19888a9b" title="compute the flux through the FluxMeter volume surface based upon the microtubules in tubeMatrix ...">P1906MOL_MOTOR_VolSurface::fluxMeter(gsl_matrix * tubeMatrix)</a> to obtain the data.  </p>
</dd>
<dt><a class="anchor" id="_todo000003"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___extended_diffusion.html#a186741e94dd82246f54815e72454959e">ns3::P1906MOL_ExtendedDiffusion::P1906MOL_ExtendedDiffusion</a>  (void)</dt>
<dd><p class="startdd">transmission belongs in Perturbation </p>
<p>diffusion-wave is a Message Carrier </p>
<p class="enddd">receive should be part of Specificity  </p>
</dd>
<dt><a class="anchor" id="_todo000005"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___extended_diffusion.html#aec14e3a8b8ff8c0ed4eada48affa66f9">ns3::P1906MOL_ExtendedDiffusion::receive</a>  (double rt, <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___pos.html" title="Class implementing a generic nanotube structure. ">P1906MOL_MOTOR_Pos</a> rp)</dt>
<dd>wv is a growing list of waves, will need to remove waves that have reached equilibrium (or disseminated)  </dd>
<dt><a class="anchor" id="_todo000004"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___extended_diffusion.html#aa97c5cb6a6edca754a84800553eb7129">ns3::P1906MOL_ExtendedDiffusion::transmit</a>  (double tt, double D, double ic, <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___pos.html" title="Class implementing a generic nanotube structure. ">P1906MOL_MOTOR_Pos</a> ip)</dt>
<dd>wv is a growing list of waves, will need to remove waves that have reached equilibrium (or disseminated)  </dd>
<dt><a class="anchor" id="_todo000019"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___motor.html#ac60d2e25c0eb6a6df2110be5c9ae5326">ns3::P1906MOL_Motor::getTime</a>  ()</dt>
<dd>return the propagation delay for a motor  </dd>
<dt><a class="anchor" id="_todo000008"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___microtubules_field.html#a01ba0902836e78ee4373464af6190c8d">ns3::P1906MOL_MOTOR_MicrotubulesField::genTubes</a>  ()</dt>
<dd>get actual tube graph properties from biologist  </dd>
<dt><a class="anchor" id="_todo000006"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___microtubules_field.html#a283319b57a991fc02f3421b65f1c36a9">ns3::P1906MOL_MOTOR_MicrotubulesField::P1906MOL_MOTOR_MicrotubulesField</a>  ()</dt>
<dd><p class="startdd">consider implementing Random Markov Field (RMF) for analysis of motor motion </p>
<p>curve fit to tube segments to obtain vector field equation (vector field reconstruction) is currently done in separate Mathematica code </p>
<p>relate structural entropy to energy, force, and chemical complexity </p>
<p>add convection-diffusion using vector field lines </p>
<p>could grow tubes from alternating ends so that starting point is in the center </p>
<p>consider many motors operating simultaneously: they would need to update simultaneously </p>
<p>plot structural entropy versus delay </p>
<p>plot binding time versus delay </p>
<p>plot distance travelled versus delay, structural entropy, etc. </p>
<p class="enddd">plot motor starting in random location versus time to reach destination as function of tube structure  </p>
</dd>
<dt><a class="anchor" id="_todo000010"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___microtubules_field.html#ad2d675a114cabd654ef61a134625f8bc">ns3::P1906MOL_MOTOR_MicrotubulesField::unitTest_ReflectiveBarrier</a>  ()</dt>
<dd>add test if the ReflectiveBarrier includes the Receiver destination volume, if not, warn that motion will continue forever  </dd>
<dt><a class="anchor" id="_todo000009"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___microtubules_field.html#af70c7a4ee0712c1b022766705dd8e037">ns3::P1906MOL_MOTOR_MicrotubulesField::unitTest_VolSurface</a>  ()</dt>
<dd>test the volume surface as a flux meter and later as a compartmentalization volume  </dd>
<dt><a class="anchor" id="_todo000014"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___motion.html#a73746852d723d20d55f78b0f1775e6b1">ns3::P1906MOL_MOTOR_Motion::ComputePropagationDelay</a>  (Ptr&lt; P1906CommunicationInterface &gt; src, Ptr&lt; P1906CommunicationInterface &gt; dst, Ptr&lt; P1906MessageCarrier &gt; message, Ptr&lt; P1906Field &gt; field)</dt>
<dd>remove before submitting  </dd>
<dt><a class="anchor" id="_todo000012"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___motion.html#a5971f8ab4024eea74a4a9a9868c13c1e">ns3::P1906MOL_MOTOR_Motion::motorWalk</a>  (Ptr&lt; P1906MessageCarrier &gt; carrier, gsl_rng *r, gsl_vector *startPt, vector&lt; P1906MOL_MOTOR_Pos &gt; &amp;pts, gsl_matrix *tubeMatrix, size_t segPerTube, vector&lt; P1906MOL_MOTOR_VolSurface &gt; &amp;vsl)</dt>
<dd><p class="startdd">set realistic binding probability </p>
<p class="enddd">set tube radius (thickness) globally  </p>
</dd>
<dt><a class="anchor" id="_todo000015"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___tube.html#a3711a030f0d0e643f6db3ef0a858f734">ns3::P1906MOL_MOTOR_Tube::genTube</a>  (struct <a class="el" href="structtube_characteristcs__t.html" title="systemic properties of the microtubule network ">tubeCharacteristcs_t</a> *ts, gsl_rng *r, gsl_matrix *segMatrix, gsl_vector *startPt)</dt>
<dd>randomize initial tube orientations  </dd>
<dt><a class="anchor" id="_todo000016"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___tube.html#aa9faa9a6104a50aaef4ca9277abbc23a">ns3::P1906MOL_MOTOR_Tube::getPersistenceLength</a>  ()</dt>
<dd>never implemented; may not be needed  </dd>
<dt><a class="anchor" id="_todo000017"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___tube.html#aa67d7e1c9c59f557a6bc0ad358a5e75e">ns3::P1906MOL_MOTOR_Tube::startPt</a>  </dt>
<dd>get actual tube graph properties from a biologist  </dd>
<dt><a class="anchor" id="_todo000018"></a>Member <a class="el" href="classns3_1_1_p1906_m_o_l___m_o_t_o_r___vol_surface.html#ab9de294ac38ab43f4ea3a19d19888a9b">ns3::P1906MOL_MOTOR_VolSurface::fluxMeter</a>  (gsl_matrix *tubeMatrix)</dt>
<dd>incorporate direction and motor rate along tube </dd>
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